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Yorodumi- PDB-1xux: Structural rationalization of a large difference in RNA affinity ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xux | ||||||||||||||||||
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Title | Structural rationalization of a large difference in RNA affinity despite a small difference in chemistry between two 2'-O-modified nucleic acid analogs | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / RNA mimetic methylamino amide analog | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | Authors | Pattanayek, R. / Sethaphong, L. / Pan, C. / Prhavc, M. / Prakash, T.P. / Manoharan, M. / Egli, M. | Citation | Journal: J.Am.Chem.Soc. / Year: 2004 | Title: Structural rationalization of a large difference in RNA affinity despite a small difference in chemistry between two 2'-O-modified nucleic acid analogues. Authors: Pattanayek, R. / Sethaphong, L. / Pan, C. / Prhavc, M. / Prakash, T.P. / Manoharan, M. / Egli, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xux.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xux.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/1xux ftp://data.pdbj.org/pub/pdb/validation_reports/xu/1xux | HTTPS FTP |
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-Related structure data
Related structure data | 1xuwC 1dplS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3132.083 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetically created #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.39 Å3/Da / Density % sol: 71.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1mM 10mer, 40mM sodium cacodylate, 12 mM spermine 4HCl, 80mM potassium chloride, 10% MPD, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.96297 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96297 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. all: 23065 / Num. obs: 23065 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.044 |
Reflection shell | Resolution: 1.3→1.38 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.073 / Num. unique all: 2093 / % possible all: 49.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DPL Resolution: 1.3→30 Å / Cross valid method: throughtout / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.3→30 Å
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Refine LS restraints |
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